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Sample GSM6122994 Query DataSets for GSM6122994
Status Public on Sep 01, 2022
Title A549 cells, Control_1, 72h
Sample type SRA
Source name Lung
Organism Homo sapiens
Characteristics tissue: Lung
cell line: A549
cell type: Human non-small cell lung cancer cell
genotype: WT
treatment: untreated
Treatment protocol A549 cells was treated by B35 (2μM) or untreated for 72h
Growth protocol A549 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C
Extracted molecule total RNA
Extraction protocol RNA was harvested using TRIzol (Invitrogen, USA). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Data processing Quality control:Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools
Quantification of gene expression level:featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values and raw gene counts for each Sample
Submission date May 08, 2022
Last update date Sep 02, 2022
Contact name 海蓝 黄
Phone 13318030705
Organization name Shenyang Pharmaceutical University
Street address No.103,Wenhua Street, Shenhe District
City Shengyang
State/province Liaoning
ZIP/Postal code 110000
Country China
Platform ID GPL24676
Series (1)
GSE202477 Effect of LSD1 inhibitor B35 on gene expression of A549 cells
BioSample SAMN28156554
SRA SRX15206691

Supplementary file Size Download File type/resource
GSM6122994_control_1.txt.gz 355.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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